Gaps were removed from the final alignment using trimAl v1.3 [ 35] with a consistency and gap score cutoffs of 0.1667 and 0.1, respectively.
Positions in the alignment containing a high number of gaps were eliminated using trimAl [ 44], with a consistency cutoff of 0.1667 and a gap score cutoff of 0.1.
The resulting alignment of each family was trimmed using trimAl v1.3 [ 103] using a consistency cutoff of 0.1667 and a gap score cutoff of 0.1.
The six resulting alignments were then combined using M-COFFEE (T-Coffee v8.80) (Wallace et al. 2006) and trimmed using trimAl v1.3 (Capella-Gutiérrez et al. 2009) with a consistency cutoff of 0.1667 and a gap score cutoff of 0.1.
The resulting combined alignment was subsequently trimmed with trimAl v1.3 [ 89] using a consistency score cutoff of 0.1667 and a gap score cutoff of 0.9.
This score can be a gap score (S g ), a similarity score (S s ) or a consistency score (S c ).
Additionally, significant time gaps existed between the analyses of each sample set, and some MFs may have lacked a consistency that would withstand minor technical variability between analyses.
